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Thermo Fisher Scientific TaqCheck User Manual

TaqCheck™ SARS-CoV-2 Fast PCR Assay
USER GUIDE
Catalog Numbers A47693
Publication Number MAN0019745
Revision A.0
For Research Use Only. Not for use in diagnostic procedures.
The information in this guide is subject to change without notice.
DISCLAIMER: T
O THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.
Revision history: Pub. No. MAN0019745
Revision Date Description
A.0 27 January 2021 New document.
Important Licensing Information: These pr
oducts may be covered by one or more Limited Use Label Licenses. By use of these
products, you accept the terms and conditions of all applicable Limited Use Label Licenses.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Tween is a registered trademark of Croda Americas, Inc.
©2021 Thermo Fisher Scientific Inc. All rights reserved.
Contents
■
CHAPTER 1 Product information .................................................. 4
Product description ............................................................. 4
Contents and storage ............................................................ 5
Required materials not supplied ................................................... 5
■
CHAPTER 2 Methods ............................................................... 8
General laboratory recommendations .............................................. 8
Guidelines for sample collection and storage ....................................... 8
Prepare saliva samples .......................................................... 9
Before you begin ........................................................... 9
Prepare 96‑well plates with TBE Buer‑Tween®-20 Detergent (TBE‑T) mix ......... 10
Prepare the samples ....................................................... 10
Prepare RT-PCR reactions ...................................................... 11
Guidelines for RT-PCR ..................................................... 11
Prepare the RT‑PCR reactions (96‑well reaction plate) .......................... 11
Prepare the RT‑PCR reactions (384‑well reaction plate) ......................... 13
Set up and run the real‑time PCR ................................................ 15
Analyze data .................................................................. 16
■
APPENDIX A Safety ............................................................... 18
Chemical safety ................................................................ 19
Biological hazard safety ......................................................... 21
■
APPENDIX B Documentation and support ...................................... 22
Related documentation ......................................................... 22
Customer and technical support ................................................. 22
Limited product warranty ........................................................ 23
TaqCheck™ SARS-CoV-2 Fast PCR Assay User Guide
3
1
Product description .................................................................... 4
■
Contents and storage .................................................................. 5
■
Required materials not supplied ......................................................... 5
■
IMPORTANT! Before using this product, read and understand the information in the “Safety” appendix
in this document.

Product description

The TaqCheck™ SARS-CoV-2 Fast PCR Assay is a multiplex real‑time RT‑PCR assay for the detection of SARS-CoV-2 viral RNA in human raw saliva samples. The assay has a multi-target design that compensates for emerging SARS-CoV-2 variants and mutations to provide confidence in results. The assay contains primer and probe sets specific to the following targets:

Product information

Table 1 Assay targets, dyes, and quenchers
Target Dye Quencher
SARS-CoV-2 N gene
VIC™ dye QSY™ quencher
SARS-CoV-2 S gene
Human RNase P RPP30 gene
[1]
S
erves as an internal positive control to monitor sample quality.
The assay requires the following components:
•
TaqCheck™ SARS‑CoV‑2 Control—RNA control that contains SARS-CoV-2 N protein and S protein target regions
•
TaqCheck™ SARS‑CoV‑2 Control Dilution Buer—Dilution buer for the control
•
TaqPath™ 1-Step RT-qPCR Master Mix, CG
For catalog numbers and storage conditions, see “Contents and storage”.
IMPORTANT! It is the r
Assay to design and validate their own experimental design and analysis parameters.
[1]
esponsibility of the laboratories using the TaqCheck™ SARS-CoV-2 Fast PCR
FAM™ dye QSY™ quencher
4
TaqCheck™ SARS-CoV-2 Fast PCR Assay User Guide
Chapter 1 Product information

Contents and storage

Contents and storage
The items listed in the following table are required for the TaqCheck™ SARS-CoV-2 Fast PCR Assay. The items listed are sucient for 1,200 reactions.
Kit or product Cat. No. Amount Storage
TaqCheck™ SARS-CoV-2 Fast PCR Assay A47693 690 µL –30°C to –10°C
TaqCheck™ SARS‑CoV‑2 Control 956127 3 × 10 µL ≤ –70°C
1
TaqCheck™ SARS‑CoV‑2 Control Dilution
Buer
TaqPath™ 1-Step RT-qPCR Master Mix, CG
A50486 3 × 250 µL –30°C to –10°C
•
A15299
•
A15300

Required materials not supplied

Unless otherwise indicated, all materials are available through thermofisher.com. "MLS" indicates that the material is available from fisherscientific.com or another major laboratory supplier.
Catalog numbers that appear as links open the web pages for those products.
Item Source
Real-time PCR instrument and software
An Applied Biosystems™ real-time PCR instrument compatible with the dyes listed in Table 1 on page 4.
The assay was tested with the following instruments:
•
Applied Biosystems™ 7500 Fast Real‑Time PCR Instrument
•
Applied Biosystems™ QuantStudio™ 5 Real‑Time PCR Instrument, 96‑well, 0.2-mL block
•
Applied Biosystems™ QuantStudio™ 5 Real‑Time PCR Instrument, 384‑well block
•
Applied Biosystems™ QuantStudio™ 7 Flex Real-Time PCR Instrument, 384‑well block
•
5 × 1 mL
•
1 × 10 mL
–30°C to –10°C
Contact your local sales oce
(Recommended) QuantStudio™ Design and Analysis Software v2.5
[1]
or later
Equipment
Laboratory freezers
•
–30°C to –10°C
•
≤ –70°C
TaqCheck™ SARS-CoV-2 Fast PCR Assay User Guide
thermofisher.com/qpcrsoftware
•
MLS
•
thermofisher.com/tsx
5
Chapter 1 Product information
1
Required materials not supplied
(continued)
Item Source
BSL-2 biological safety cabinet, such as Herasafe™ 2030i Class 2 A2 Biological Safety Cabinets
•
MLS
•
thermofisher.com
Centrifuge (capable of achieving 1,400 × g), such as Megafuge™ 8 Small Benchtop Centrifuge Series or Multifuge X4 Pro Centrifuge Series
Microcentrifuge, such as Pico™ 17 Microcentrifuge
Laboratory mixer, vortex or equivalent, such as Digital Vortex Mixers
Single and multichannel adjustable pipettors (2.00 µL to 1,000.0 µL)
Cold block (96‑well or 384‑well) or ice MLS
Heat block or water bath (capable of reaching 95°C), such as Touch Screen Dry Bath/Block Heater or Precision™ General Purpose Baths
Liquid handler (if needed for automation)
Kits and reagents
TBE Buer (Tris-borate-EDTA) (10X) B52, or equivalent
Tween®-20 Sur
fact-Amps™ Detergent Solution 28320
[2]
•
MLS
•
thermofisher.com
•
MLS
•
thermofisher.com
•
MLS
•
thermofisher.com
•
www.thermofisher.com/cliptip
•
thermofisher.com/finnpipette
•
MLS
•
thermofisher.com
MLS
•
AM9938 (1 x 100 mL)
Nuclease-free Water (not DEPC-Treated)
70% Isopropanol spray or wipes MLS
Tubes, plates, and other consumables
(Recommended) S sample collection
IMPORTANT! Do not use tubes that contain pr
Reservoir for multichannel pipettes MLS
Sterile aerosol barrier (filtered) pipette tips thermofisher.com/pipettetips
96‑well plate (for preparing saliva samples, not for RT-PCR) AB0796, or equivalent
terile tube with leak‑proof, screw‑top lid for
[3]
eservative.
6
•
AM9932 (1 x 1,000 mL)
One of the following, or equivalent:
•
AM12500
•
339650
•
14-959-49B (fisherscientific.com)
TaqCheck™ SARS-CoV-2 Fast PCR Assay User Guide
Chapter 1 P
Required materials not supplied
roduct information
(continued)
Item Source
•
4346906 (with barcode)
•
MicroAmp™ Fast Optical 96-Well Reaction Plate, 0.1 mL
MicroAmp™ Optical 96-Well Reaction Plate, 0.2 mL
MicroAmp™ Optical 384-Well Reaction Plate
4366932 (with barcode)
•
4346907 (without barcode)
•
4306737 (with barcode)
•
4326659 (with barcode)
•
N8010560 (without barcode)
•
4316813 (without barcode)
•
4309849 (with barcode)
•
4326270 (with barcode)
•
4343814 (with barcode)
•
4343370 (without barcode)
MicroAmp™ Clear Adhesive Film 4306311
1
MicroAmp™ Optical Adhesive Film 4311971, 4360954
MicroAmp™ Adhesive Film Applicator 4333183
Nonstick, RNase-free microcentrifuge tubes (1.5 mL and 2.0 mL) thermofisher.com/microtubes
DNase and RNase‑free tubes for mixing reagents (capable of mixing 5 mL and 50 mL)
Nunc™ 1.8‑mL Ext
ernally-Threaded Universal Tubes 374502
thermofisher.com
Nalgene™ General Long-Term Storage Cryogenic Tubes, 0.2 mL 5000-0020
Nunc™ Biobanking and Cell Culture Cryogenic Tubes, 4.5 mL 337516
•
Sterilin™ Certified Universal Containers – RNase, DNase, human DNA and Pyrogen Free, 30 mL
[1]
U
se of QuantStudio™ Design and Analysis Software v2.5 is recommended, but not required. It is the responsibility of the laboratories using the
assay to design and validate their own experimental design and analysis parameters.
[2]
Follow the guidelines provided by the manufacturer.
[3]
The use of the tubes listed in the table is recommended, but not required. Laboratories are responsible for validating their sample collection and preparation procedures for use with the assay.
30APPRN (Unlabelled)
•
30BPPRN (Graduated label)
TaqCheck™ SARS-CoV-2 Fast PCR Assay User Guide
7
2
General laboratory recommendations .................................................... 8
■
Guidelines for sample collection and storage ............................................. 8
■
Prepare saliva samples ................................................................. 9
■
Prepare RT-PCR reactions ............................................................. 11
■
Set up and run the real‑time PCR ....................................................... 15
■
Analyze data ......................................................................... 16
■

General laboratory recommendations

•
Implement standard operating procedures in your laboratory to prevent contamination, such as the following:
–
Frequent glove changes
–
Frequent decontamination of surfaces, equipment, and pipettes with 10% bleach or decontamination solution, followed by 70% ethanol
–
Use of ultraviolet light during biosafety cabinet decontamination (when available)
•
Saliva samples should always be treated as if infectious and/or biohazardous in accordance with safe laboratory procedures.
•
To prevent degradation, keep master mixes, assays, and controls on ice or in cold blocks while in use. Limit freeze-thaw cycles.
•
Aliquot reagents to prevent stock contamination and reduce the number of freeze-thaw cycles.
•
To ensure reliable performance of the real‑time PCR instrument, perform preventive maintenance according to the instructions provided by the manufacturer in the instrument documentation (see “Related documentation” on page 22).

Methods

Guidelines for sample collection and storage

•
Collect saliva sample in a collection device with a leak‑proof, screw‑top lid.
IMPORTANT! Do not collect saliva using a device that contains preservative solution.
•
Collect a minimum of 1 mL saliva.
8
TaqCheck™ SARS-CoV-2 Fast PCR Assay User Guide
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